Summary Neuronal ceroid lipofuscinoses (NCLs), also known as Batten disease, constitute a group of the most common neurodegenerative lysosomal storage disorders (LSDs) without an effective treatment. Mutations in >13 different genes (called CLNs) underlie pathogenesis of various forms of NCLs. The infantile NCL (INCL) is one of the most devastating neurodegenerative LSDs caused by mutations in the CLN1 gene, which encodes palmitoyl-protein thioesterase-1 (PPT1). PPT1 is a lysosomal thioesterase that depalmitoylates S-acylated proteins facilitating their degradation by lysosomal hydrolases. The deficiency of PPT1 prevents degradation of S-acylated proteins (constituents of ceroid) causing accumulation of ceroid in lysosomes, which leads to INCL. There are several pathological features (e.g. elevated lysosomal pH, accumulation of intracellular autofluorescent material, GRODs, seizures and short life span) that are common to all NCLs. These features prompted us to investigate whether there are common pathogenic mechanisms shared by all NCLs. We have previously reported that cathepsin D (CD)-deficiency is a common pathogenic link between congenital NCL (CNCL), caused by mutations in the CLN10 gene encoding cathepsin D (CD), and INCL caused by mutations in the CLN1 gene encoding PPT1. Thus, in both INCL (CLN1-disease) and CNCL (CLN10-disease) lysosomal accumulation of ceroid contributes to pathogenesis. Defective lysosomal acidification contributes to pathogenesis of virtually all lysosomal storage disorders (LSDs). It is also a contributory factor in the pathogenesis of common neurodegenerative diseases like Alzheimer's and Parkinson's. Despite the critical importance of lysosomal acidification, the mechanism(s) underlying the dysregulation of lysosomal acidification in these diseases remains poorly understood. The cellular proton pump, vacuolar-ATPase (v-ATPase), is known to regulate lysosomal pH. v-ATPase is a multisubunit protein complex composed of cytosolic V1-sector and lysosomal membrane-anchored V0-sector. The V1 subunit breaks down ATP generating energy required for the V0 sector to transport protons from the cytoplasm to the lysosomal lumen to maintain acidic pH. We found that in the brain tissues of Cln1-/- mice, which mimic INCL, reduced v-ATPase activity correlated with elevated lysosomal pH. Moreover, v-ATPase subunit a1 of the V0 sector (V0a1) requires S-palmitoylation for interacting with adaptor protein-2 (AP-2) and AP-3, respectively, for trafficking to the lysosomal membrane. Unexpectedly, we discovered that in Ppt1-deficient Cln1-/- mice, V0a1 is misrouted to the plasma membrane instead of its normal location on lysosomal membrane. Notably, treatment of the Cln1-/- mice with a thioesterase (Ppt1)-mimetic, non-toxic small molecule, N-tert (Butyl) hydroxylamine (NtBuHA), ameliorated this defect. Our findings reveal an unanticipated role of Cln1 in regulating lysosomal targeting of V0a1 and suggest that varying factors adversely affecting v-ATPase activity may dysregulate lysosomal acidification in other LSDs including various forms of the NCLs and common neurodegenerative diseases. As part of a project studying the treatment benefits of a combination of cysteamine bitartrate and N-acetyl cysteine, we made serial measurements of patients' brain volumes with MR imaging. Ten patients with infantile neuronal ceroid lipofuscinosis participating in a treatment/follow-up study underwent brain MR imaging that included high-resolution T1-weighted images. After manual placement of a mask delineating the surface of the brain, a maximum-likelihood classifier was applied to determine total brain volume, further subdivided as cerebrum, cerebellum, brain stem, and thalamus. Patients' brain volumes were compared with those of a healthy population. Major subdivisions of the brain followed similar trajectories with different timing. The cerebrum demonstrated early, rapid volume loss and may never have been normal postnatally. The thalamus dropped out of the normal range around 6 months of age;the cerebellum, around 2 years of age; and the brain stem, around 3 years of age. Rapid cerebral volume loss was expected on the basis of previous qualitative reports. Because our study did not include a nontreatment arm and because progression of brain volumes in INCL has not been previously quantified. However, the level of quantitative detail in this study allows it to serve as a reference for evaluation of future therapeutic interventions. In virtually all neurodegenerative disorders, neuronal death is followed by proliferation and activation of astrocytes and microglia (hereafter called astroglia). These activated astroglia secrete cytokines that are neurotoxic causing death of viable neurons, which leads to progressive neurodegeneration. Using two different mouse models of INCL, we found that astroglia activation occurs in an age-dependent manner. It has recently been reported that cytokines secreted by the activated microglia stimulates the differentiation and activation of a special type of astrocytes called Astrocyte A1. These astrocytes secrete as yet uncharacterized, extremely potent neurotoxins, which leads to further neuronal death and progressive neurodegeneration. Our ongoing research is attempting to isolate homogeneous cultures of Astrocyte A1 and characterize the neurotoxins. We hope to study how these neurotoxins mediate neuronal death in Cln1-/- mice and screen small molecules to find those that neutralize these toxins. Such compounds may have neuroprotective activities with potential for use as a therapeutic agent for INCL and perhaps other neurodegenerative diseases. A US Patent (US 20140148513 A1), entitled Small molecule therapeutic compounds targeting thioesterase deficiency disorders and methods of using the same has been granted. Currently, preclinical studies are being conducted to obtain FDA approval for conducting a clinical trial in INCL patients.